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J Chem Theory Comput. 2019 Apr 9;15(4):2734-2742. doi: 10.1021/acs.jctc.9b00054. Epub 2019 Mar 12.

Development and Testing of the OPLS-AA/M Force Field for RNA.

Author information

1
Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , United States.

Abstract

Significant improvements have been made to the OPLS-AA force field for modeling RNA. New torsional potentials were optimized based on density functional theory (DFT) scans at the ωB97X-D/6-311++G(d,p) level for potential energy surfaces of the backbone α and γ dihedral angles. In combination with previously reported improvements for the sugar puckering and glycosidic torsion terms, the new force field was validated through diverse molecular dynamics simulations for RNAs in aqueous solution. Results for dinucleotides and tetranucleotides revealed both accurate reproduction of 3 J couplings from NMR and the avoidance of several unphysical states observed with other force fields. Simulations of larger systems with noncanonical motifs showed significant structural improvements over the previous OPLS-AA parameters. The new force field, OPLS-AA/M, is expected to perform competitively with other recent RNA force fields and to be compatible with OPLS-AA models for proteins and small molecules.

PMID:
30807148
PMCID:
PMC6585454
[Available on 2020-04-09]
DOI:
10.1021/acs.jctc.9b00054
[Indexed for MEDLINE]

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